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X-RAY STRUCTURE OF SMYD3 IN COMPLEX WITH the benzodiazepine-based probe BAY-6035
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other previously solved inhouse structure
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 8 % PEG 3350, 50 mM magnesium formate, 100 mM Tris pH 7.5
Crystal Properties Matthews coefficient Solvent content 2.22 44.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.497 α = 90 b = 66.166 β = 90 c = 107.165 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M 2017-06-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.91840 BESSY 14.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.52 41.64 99.5 0.997 10 5.3 68061
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.52 1.61 0.718
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT previously solved inhouse structure 1.52 41.64 65960 2100 99.48 0.1596 0.1575 0.157 0.2251 0.2252 RANDOM 18.237
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] -0.18 1.15 -0.98
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.063 r_dihedral_angle_4_deg 19.014 r_dihedral_angle_3_deg 13.403 r_dihedral_angle_1_deg 6.795 r_rigid_bond_restr 4.609 r_angle_refined_deg 1.991 r_angle_other_deg 1.585 r_chiral_restr 0.113 r_bond_refined_d 0.016 r_gen_planes_refined 0.015
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.063 r_dihedral_angle_4_deg 19.014 r_dihedral_angle_3_deg 13.403 r_dihedral_angle_1_deg 6.795 r_rigid_bond_restr 4.609 r_angle_refined_deg 1.991 r_angle_other_deg 1.585 r_chiral_restr 0.113 r_bond_refined_d 0.016 r_gen_planes_refined 0.015 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3390 Nucleic Acid Atoms Solvent Atoms 544 Heterogen Atoms 59
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XSCALE data scaling PHASER phasing